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* fix quoting to a lot of patch callsMike Frysinger2017-01-201-1/+1
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* sci-biology/rebase: Drop oldJustin Lecher2017-01-152-47/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/abyss: only openmpi is supportedMartin Mokrejš2017-01-151-7/+16
| | | | Closes: https://github.com/gentoo/gentoo/pull/3414
* sci-biology/mummer: Version bump to 3.9.4_alphaDavid Seifert2017-01-152-0/+84
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/rebase: ppc stable wrt bug #604448Agostino Sarubbo2017-01-151-1/+1
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/wgs-assembler: Drop oldPacho Ramos2017-01-154-212/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/mira: Removed unused patches.Lars Wendler2017-01-133-132/+0
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/mira: Bump to EAPI-6. Ebuild cleanup.Lars Wendler2017-01-132-10/+39
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/mira: Update flex-2.6.3 fix; add cmath headerNicholas Vinson2017-01-132-2/+18
| | | | | | | | | | | | | Another round of testing discovered that caf_flexer.cc is also a pre-generated lexer. The commit updates the ebuild to remove that file as well. The file abs.C fails to find the pow() function. Modern versions of C++ store the header for that function in cmath. The file is updated to include that header. Gentoo-bug: 585942 Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3442
* sci-biology/mira: Adjusted sys-devel/flex dependency.Lars Wendler2017-01-111-1/+1
| | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/mira: Force rebuild of lexer C++ source filesNicholas Vinson2017-01-111-1/+12
| | | | | | | | Upstream ships pregenerated C++ source files for its lexers. These files fail to compile under newer versions of GCC. This update forces them to be rebuilt by removing them before compilaiton starts. Package-Manager: Portage-2.3.3, Repoman-2.3.1
* sci-biology/rebase: x86 stable wrt bug #604448Agostino Sarubbo2017-01-041-1/+1
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: amd64 stable wrt bug #604448Agostino Sarubbo2017-01-041-2/+2
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="amd64" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: Drop oldJustin Lecher2017-01-026-235/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/biopython: Drop oldJustin Lecher2017-01-024-154/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: Version BumpJustin Lecher2017-01-022-0/+47
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/rebase: x86 stable wrt bug #590146Agostino Sarubbo2017-01-021-1/+1
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/biopython: x86 stable wrt bug #584210Agostino Sarubbo2017-01-021-1/+1
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/rebase: ppc stable wrt bug #590146Agostino Sarubbo2017-01-011-2/+2
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/biopython: ppc stable wrt bug #584210Agostino Sarubbo2017-01-011-2/+2
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="ppc" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/seqan: x86 stable wrt bug #525628Agostino Sarubbo2016-12-291-1/+1
| | | | | | Package-Manager: portage-2.3.0 RepoMan-Options: --include-arches="x86" Signed-off-by: Agostino Sarubbo <ago@gentoo.org>
* sci-biology/seqan: amd64 stable wrt bug #525628Aaron Bauman2016-12-261-1/+1
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* sci-biology/clustal-omega: Version BumpJustin Lecher2016-12-232-0/+39
| | | | | | | Thanks Fabian Sievers notifying me Package-Manager: Portage-2.3.3, Repoman-2.3.1 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/abyss: Remove oldDavid Seifert2016-12-2011-310/+0
| | | | | Package-Manager: Portage-2.3.3, Repoman-2.3.1 Closes: https://github.com/gentoo/gentoo/pull/3183
* sci-biology/rebase-1604-r0: stable on amd64Tobias Klausmann2016-12-201-1/+1
| | | | Gentoo-Bug: 587822
* sci-biology/bamtools: Remove oldDavid Seifert2016-12-154-104/+0
| | | | | Package-Manager: portage-2.3.3 Closes: https://github.com/gentoo/gentoo/pull/3120
* sci-biology/bamtools: Version bump to 2.4.1David Seifert2016-12-144-0/+314
| | | | | | | | Gentoo-bug: 550144, 596208 * Make C++ mode agnostic * Unbundle jsoncpp and use more modern versions Package-Manager: portage-2.3.3
* sci-biology/seqan: Add blocker for older SLOTsDavid Seifert2016-12-141-17/+23
| | | | | | Gentoo-bug: 602508 Package-Manager: portage-2.3.3
* sci-biology/rebase: Version BumpJustin Lecher2016-12-092-0/+47
| | | | | Package-Manager: portage-2.3.3 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/gmap: Clean metadata.xmlPacho Ramos2016-11-271-4/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/gmap: Drop old (#597984)Pacho Ramos2016-11-273-74/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/bedtools: This needs slot 0 of samtools (#597982)Pacho Ramos2016-11-271-1/+1
| | | | Package-Manager: portage-2.3.2
* sci-biology/treeviewx: Drop oldPacho Ramos2016-11-251-32/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/treeviewx: x86 stable, bug #584034Pacho Ramos2016-11-251-2/+2
| | | | Package-Manager: portage-2.3.2
* sci-biology/meme: Add $(DESTDIR) to install hooksDavid Seifert2016-11-201-1/+24
| | | | | | Gentoo-bug: 600316 Package-Manager: portage-2.3.2
* sci-biology/meme: Version bump to 4.11.2_p2David Seifert2016-11-195-0/+872
| | | | | | | | | | Gentoo-bug: 599860 * EAPI=6 * Install documentation and examples correctly * Install perl and python modules correctly * Add missing perl runtime dependencies Package-Manager: portage-2.3.2
* sci-biology/bioperl-run: Fix overlong DESCRIPTIONDavid Seifert2016-11-182-4/+4
| | | | Package-Manager: portage-2.3.2
* sci-biology/biogrep: Remove old ebuildsDavid Seifert2016-11-182-43/+0
| | | | Package-Manager: portage-2.3.2
* sci-biology/biogrep: Port to EAPI=6David Seifert2016-11-182-0/+37
| | | | | | | * Add USE="doc" and USE="examples" * Run 'eautoreconf' to modernize configure script Package-Manager: portage-2.3.2
* sci-biology/arb: Fix overlong DESCRIPTIONDavid Seifert2016-11-183-6/+6
| | | | Package-Manager: portage-2.3.2
* sci-biology/abyss: bump up to 2.0.2, bug #596018Sergei Trofimovich2016-11-063-1/+49
| | | | | | | | | Fixes gcc-6 and boost-1.62 build failures. Reported-by: Toralf Förster Bug: https://bugs.gentoo.org/596018 Package-Manager: portage-2.3.2
* global: Drop dead implementations from PYTHON_COMPATMichał Górny2016-11-014-4/+4
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* Revert "Temporarily remove Manifest files that were at risk of having broken ↵Michael Palimaka2016-10-311-0/+6
| | | | | | ChangeLog entries." This reverts commit 48b59c28052dbc9a1c410a8a5d93c1cc3c8c8d4b.
* Temporarily remove Manifest files that were at risk of having broken ↵Michael Palimaka2016-10-311-6/+0
| | | | | | | | | ChangeLog entries. This commit will be immediately reverted. The intention is to force the mtime to be bumped causing the updated Manifest to be propagated to mirrors. Gentoo-bug: 577722
* sci-biology/rebase: Bump to latest DBJustin Lecher2016-10-292-0/+47
| | | | | Package-Manager: portage-2.3.2 Signed-off-by: Justin Lecher <jlec@gentoo.org>
* sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2David Seifert2016-10-093-0/+205
| | | | | | | | | Gentoo-bug: 328911, 586960 * EAPI=6 * Introduce SLOT=2 and rename binaries and static libraries Package-Manager: portage-2.3.1
* sci-biology/hmmer: Version bump to 3.1_beta2David Seifert2016-10-094-0/+470
| | | | | | | | * EAPI=6 * Make perl shebangs portable * Install headers into 'hmmer3' subdir Package-Manager: portage-2.3.1
* sci-biology/tophat: Do not wrap scriptsDavid Seifert2016-10-031-2/+2
| | | | Package-Manager: portage-2.3.1
* sci-biology/samtools: Use 'python-single-r1' instead of 'python-r1'David Seifert2016-10-031-17/+21
| | | | Package-Manager: portage-2.3.1
* sci-biology/consed: Remove old ebuildsDavid Seifert2016-10-033-165/+0
| | | | Package-Manager: portage-2.3.1